Question: RPKM to FPKM conversion
0
gravatar for kanwarjag
3.2 years ago by
kanwarjag950
United States
kanwarjag950 wrote:

I have RNAseq data as RPKM values (tumor vs normal)  since data is paired end how could I convert to FPKM values. 

Thanks

 

rna-seq • 3.2k views
ADD COMMENTlink modified 3.2 years ago by michael.ante3.2k • written 3.2 years ago by kanwarjag950
1

You may/should not convert RPKM to FPKM. You need to recalculate FPKM from BAM file. As suggested below, if you just divide by 2, they wont be true FPKM values as you do not knowif there are any read-pairs with only one-end mapped. And if there are many read pairs like that your FPKM value might not be true.

ADD REPLYlink modified 7 months ago by RamRS21k • written 3.2 years ago by geek_y9.4k

Thanks for the explanation

ADD REPLYlink modified 7 months ago by RamRS21k • written 3.2 years ago by kanwarjag950
2
gravatar for michael.ante
3.2 years ago by
michael.ante3.2k
Austria/Vienna
michael.ante3.2k wrote:

In case of single end data, RPKM=FPKM (Reads per kilobase per million reads and Fragments per kilobase per million reads).

In case of paired end data, you have for every read-pair one fragment. Thus, divide the RPKM by two.

ADD COMMENTlink modified 7 months ago by RamRS21k • written 3.2 years ago by michael.ante3.2k

very naive clarification should it be tumor RPKM/2 - normal RPKM/2

or it should be tumor RPKM-normal RPKM = X/2

ADD REPLYlink modified 7 months ago by RamRS21k • written 3.2 years ago by kanwarjag950

If you are looking at the ratios/fold-changes, it doesn't matter. The factor 2 is cancelled:

4:1 == 2:0.5
ADD REPLYlink modified 7 months ago by RamRS21k • written 3.2 years ago by michael.ante3.2k

got it 

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by kanwarjag950
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